Metadata-Version: 2.1
Name: SEQLinkage
Version: 1.0.2
Summary: Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data
Home-page: https://github.com/changebio/SEQLinkage/tree/master/
Author: Yin Huang, Gao Wang
Author-email: changebio@yeah.net
License: Apache Software License 2.0
Keywords: CHP Linkage Analysis
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Developers
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: License :: OSI Approved :: Apache Software License
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Provides-Extra: dev
License-File: LICENSE

# SEQLinkage
> Collapsed Haplotype Pattern Method for Linkage Analysis of Next-Generation Sequencing Data


## Pre-requisites

Make sure you install the pre-requisited before running seqlink:

```
conda install -c conda-forge xeus-cling
conda install -c anaconda swig 
pip install egglib
git clone https://github.com/statgenetics/cstatgen.git
cd cstatgen
python setup.py install
```

## Install

`pip install SEQLinkage`

## How to use

### 1. Test on seqlinkage-example

```
seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMBPt8 --jobs 8

seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMB0 --jobs 8 --bin 0

seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz -f MERLIN --output RMB1 --jobs 8 --bin 1

seqlink --fam seqlinkage-example.fam --vcf seqlinkage-example.vcf.gz --freq EVSEAAF -o LinkageAnalysis -K 0.001 --moi AR -W 0 -M 1 --theta-max 0.5 --theta-inc 0.05 -j 8 --run-linkage
```

### 2. Test on AD family

```
seqlink --fam data/mwe_normal_fam.csv --vcf data/first1000snp_full_samples.vcf.gz -f LINKAGE --blueprint data/genemap.hg38.txt --freq AF -K 0.001 --moi AD -W 0 -M 1

seqlink --fam data/mwe_normal_fam.csv --vcf data/first1000snp_full_samples.vcf.gz -f MERLIN --blueprint data/genemap.hg38.txt --freq AF
```


